Metabolic pathways modifications

Metabolic pathways are regulated by rapid mechanisms affecting the activity of existing enzymes, eg, allosteric and covalent modification (often in response to hormone action) and slow mechanisms affecting the synthesis of enzymes. 

However, the metabolic pathways of lutein and zeaxanthin are only beginning to be discovered. Several derivatives of dietary xanthophylls have been identified in the retina, such as 3 -epilutein, meso-zeaxanthin, 3 -oxolutein, and 3-methoxyzeaxanthin, and it has been suggested that they may be formed as a result of nonenzymatic oxidative modifications (Bernstein et al., 2001,2002b Bhosale et al., 2007b Khachik et al., 1997). The macula lutea contains predominantly meso-zeaxanthin (Figure 15.1), which is believed to originate from either oxidative modification or double bond isomerization of dietary lutein (Khachik et al., 1997, 2002). 

The activity of PK and NRPSs is often precluded and/or followed by actions upon the natural products by modifying enzymes. There exists a first level of diversity in which the monomers for respective synthases must be created. For instance, in the case of many NRPs, noncanonical amino acids must be biosynthesized by a series of enzymes found within the biosynthetic gene cluster in order for the peptides to be available for elongation by the NRPS. A second level of molecular diversity comes into play via post-synthase modification. Examples of these activities include macrocyclization, heterocyclization, aromatization, methylation, oxidation, reduction, halogenation, and glycosylation. Finally, a third level of diversity can occur in which molecules from disparate secondary metabolic pathways may interact, such as the modification of a natural product by an isoprenoid oligomer. Here, we will cover only a small subsection of... 

Fig. 1. Modification of plant metabolic pathways for the synthesis of poly(3HB) and poly(3HB-co-3HV). The pathways created or enhanced by the expression of transgenes are highlighted in bold, while endogenous plant pathways are in plain letters. The various transgenes expressed in plants are indicated in italics. The ilvA gene encodes a threonine deaminase from E. coli. The phaARe, phaBRe, and phaCRe genes encode a 3-ketothiolase, an aceto-acetyl-CoA reductase, and a PHA synthase from R. eutropha, respectively. The btkBRe gene encodes a second 3-ketothiolase isolated from R. eutropha which shows high affinity for both propionyl-CoA and acetyl-CoA [40]. PDC refers to the endogenous plant pyruvate dehydrogenase complex...

Fig. 4. Modification of plant metabolic pathways for the synthesis of poly(3HAMCL) in peroxisomes. The pathways created or enhanced by the expression of transgenes (P. aeruginosa PHA synthase and C. lanceolata decanoyl-ACP thioesterase) and of mutant alleles of plant fatty acid desaturase genes are highlighted by bold arrows and the enzymes involved underlined...

Hydrophilic hormones and other water-soluble signaling substances have a variety of biosynthetic pathways. Amino acid derivatives arise in special metabolic pathways (see p. 352) or through post-translational modification (see p. 374). Proteohormones, like all proteins, result from translation in the ribosome (see p. 250). Small peptide hormones and neuropeptides, most of which only consist of 3-30 amino acids, are released from precursor proteins by proteolytic degradation. 

Because carbohydrates are so frequently used as substrates in kinetic studies of enzymes and metabolic pathways, we refer the reader to the following topics in Ro-byt s excellent account of chemical reactions used to modify carbohydrates formation of carbohydrate esters, pp. 77-81 sulfonic acid esters, pp. 81-83 ethers [methyl, p. 83 trityl, pp. 83-84 benzyl, pp. 84-85 trialkyl silyl, p. 85] acetals and ketals, pp. 85-92 modifications at C-1 [reduction of aldehydes and ketones, pp. 92-93 reduction of thioacetals, p. 93 oxidation, pp. 93-94 chain elongation, pp. 94-98 chain length reduction, pp. 98-99 substitution at the reducing carbon atom, pp. 99-103 formation of gycosides, pp. 103-105 formation of glycosidic linkages between monosaccharide residues, 105-108] modifications at C-2, pp. 108-113 modifications at C-3, pp. 113-120 modifications at C-4, pp. 121-124 modifications at C-5, pp. 125-128 modifications at C-6 in hexopy-ranoses, pp. 128-134. 

While certain behavioral and nonbehavioral diseases are believed to be monogenic, diseases such as Huntington s, cystic fibrosis, Marfan, and Hirschsprung result in the specified disease, and the outward appearance or result (phenotype) of the disease varies between individuals. For instance, for Marfan syndrome, there is a level below which the mutant protein does not exhibit itself in an outward manner. Most of these diseases have modifier genes that cause modifications in the outward demonstration of the disease and play a key role in the clinical symptoms. Further, the particular metabolic pathways are often varied, with several of the steps being important and the importance of each mechanistic pathway may differ with every individual. 

Biosynthesis and Metabolism.—Pathways and Reactions. Two reviews of carotenoid biosynthesis discuss, respectively, the early steps and the later reactions." The former paper deals with the mechanism of formation of phytoene and the series of desaturation reactions by which phytoene is converted into lycopene, and also describes in detail the biosynthesis of bacterial C30 carotenoids. The second paper" presents details of the mechanism and stereochemistry of cyclization and the other reactions that involve the carotenoid C-1 —C-2 double bond and the later modifications, especially the introduction of oxygen functions. 

The flow of intermediates through metabolic pathways is controlled by 1bir mechanisms 1) the availability of substrates 2) allosteric activation and inhibition of enzymes 3) covalent modification of enzymes and 4) induction-repression of enzyme synthesis. This scheme may at first seem unnecessarily redundant however, each mechanism operates on a different timescale (Figure 24.1), and allows the body to adapt to a wde variety of physiologic situations. In the fed state, these regulatory mechanisms ensure that available nutrients are captured as glycogen, triacylglycerol, and protein. 

Probably the most common and widespread control mechanisms in cells are allosteric inhibition and allosteric activation. These mechanisms are incorporated into metabolic pathways in many ways, the most frequent being feedback inhibition. This occurs when an end product of a metabolic sequence accumulates and turns off one or more enzymes needed for its own formation. It is often the first enzyme unique to the specific biosynthetic pathway for the product that is inhibited. When a cell makes two or more isoenzymes, only one of them may be inhibited by a particular product. For example, in Fig. 11-1 product P inhibits just one of the two isoenzymes that catalyzes conversion of A to B the other is controlled by an enzyme modification reaction. In bacteria such as E. coli, three isoenzymes, which are labeled I, II, and III in Fig. 11-3, convert aspartate to (3-aspartyl phosphate, the precursor to the end products threonine, isoleucine, methionine, and lysine. Each product inhibits only one of the isoenzymes as shown in the figure. 

In addition to the 20 commonly occurring a-amino acids, a variety of other amino acids are found in minor amounts in proteins and in nonprotein compounds. The unusual amino acids found in proteins result from modification of the common amino acids. In a few cases these amino acids are incorporated directly into the polypeptide chains during synthesis. Most frequently the amino acid is modified after incorporation. The unusual amino acids found in nonprotein compounds are extremely varied in type and are formed by a number of different metabolic pathways (see chapter 21). 

Synthesis of most phospholipids starts from glycerol-3-phosphate, which is formed in one step from the central metabolic pathways, and acyl-CoA, which arises in one step from activation of a fatty acid. In two acylation steps the key compound phosphatidic acid is formed. This can be converted to many other lipid compounds as well as CDP-diacylglycerol, which is a key branchpoint intermediate that can be converted to other lipids. Distinct routes to phosphatidylethanolamine and phosphatidylcholine are found in prokaryotes and eukaryotes. The pathway found in eukaryotes starts with transport across the plasma membrane of ethanolamine and/or choline. The modified derivatives of these compounds are directly condensed with diacylglycerol to form the corresponding membrane lipids. Modification of the head-groups or tail-groups on preformed lipids is a common reaction. For example, the ethanolamine of the head-group in phosphatidylethanolamine can be replaced in one step by serine or modified in 3 steps to choline. 

Advanced genetic engineering techniques are being used to improve existing renewable feedstocks for the production of industrial bioproducts. In some cases, the feedstock composition is modified to increase the content of a desired component and/or decrease the content of an undesired component, whereas in others, a new metabolic pathway is inserted into the plant genes so that the modified plant produces an entirely new component. These research efforts are recent, and very little, if any, published information is currently available. However, we provide brief descriptions of the research activities to give perspective on the opportunities for new industrial bioproducts that may emerge from feedstock modification. 

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